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4d8o

Crystal Structure of the ankyrin-B ZU5-ZU5-UPA-DD tandem

Method: X-RAY DIFFRACTION Dmax: 88.5 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ankyrin-2

Homo sapiens

UniProt Q01484

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 966–1210 Chain A； UniProt 1253–1568 Fragment：residues 966-1535 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG3350, 0.2M ammonium acetate, 5% n-Octyl-beta-D-glucoside, pH 7.5, vapor diffusion, hanging drop, temperature 289K Resolution 2.20 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4D8O Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4RLV Crystal Structure of AnkB 24 Ankyrin Repeats in Complex with AnkR Autoinhibition Segment Deposited 2014-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–873（846 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.5 M ammonium sulfate, 1.0 M lithium sulfate, and 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 3.49 Å R-free 0.253
4RLY Crystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with Nav1.2 Ankyrin Binding Domain Deposited 2014-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–318（291 aa）
Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.238
4RLY Crystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with Nav1.2 Ankyrin Binding Domain Deposited 2014-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–318（291 aa）
Not recorded SO4 SULFATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.238
5Y4D Crystal Structure of AnkB Ankyrin Repeats in Complex with AnkR/AnkB Chimeric Autoinhibition Segment Deposited 2017-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3707–3718（12 aa） Fragment：UNP RESIDUES 1577-1613,UNP RESIDUES 3707-3718,UNP RESIDUES 28-693
Chain A 28–693（666 aa） Fragment：UNP RESIDUES 1577-1613,UNP RESIDUES 3707-3718,UNP RESIDUES 28-693
Not recorded SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；4 M ammonium acetate, 0.1 M Bis-Tris propane (pH 7.0)
Resolution 3.30 Å R-free 0.229
5Y4E Crystal Structure of AnkB Ankyrin Repeats R8-14 in complex with autoinhibition segment AI-b Deposited 2017-08-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 857–896（40 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483
Chain A 264–483（220 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483
Not recorded GOL GLYCEROL × 2 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1 M HEPES (pH 7.0), 1 M ammonium sulfate, 0.5% w/v PEG 8000
Resolution 2.34 Å R-free 0.233
5Y4E Crystal Structure of AnkB Ankyrin Repeats R8-14 in complex with autoinhibition segment AI-b Deposited 2017-08-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 857–896（40 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483
Chain B 264–483（220 aa） Fragment：UNP RESIDUES 857-896,UNP RESIDUES 264-483
Not recorded SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.1 M HEPES (pH 7.0), 1 M ammonium sulfate, 0.5% w/v PEG 8000
Resolution 2.34 Å R-free 0.233
5Y4F Crystal Structure of AnkB Ankyrin Repeats R13-24 in complex with autoinhibition segment AI-c Deposited 2017-08-03 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 430–873（444 aa） Fragment：UNP RESIDUES 430-873
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M CaCl2, 0.1 M HEPES (pH 7.5), 28% v/v PEG 400
Resolution 1.95 Å R-free 0.220
5Y4F Crystal Structure of AnkB Ankyrin Repeats R13-24 in complex with autoinhibition segment AI-c Deposited 2017-08-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 430–873（444 aa） Fragment：UNP RESIDUES 430-873
Not recorded CA CALCIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M CaCl2, 0.1 M HEPES (pH 7.5), 28% v/v PEG 400
Resolution 1.95 Å R-free 0.220
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)
Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614
Not recorded NI NICKEL (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)
Resolution 2.75 Å R-free 0.224
5YIR Crystal Structure of AnkB LIR/GABARAP complex Deposited 2017-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；12% w/v PEG 3350, 5 mM CoCl2, 5 mM NiCl2, 5 mM CdCl2, 5 mM MgCl2, 0.1 M HEPES buffer (pH 7.5)
Resolution 2.75 Å R-free 0.224
5YIS Crystal Structure of AnkB LIR/LC3B complex Deposited 2017-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)
Resolution 2.20 Å R-free 0.250
5YIS Crystal Structure of AnkB LIR/LC3B complex Deposited 2017-10-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1588–1614（27 aa） Fragment：UNP RESIDUES 1588-1614
Not recorded GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289 K；2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)
Resolution 2.20 Å R-free 0.250
6KZJ Crystal structure of Ankyrin B/NdeL1 complex Deposited 2019-09-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1499–1570（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；289 K；1.9M ammonium sulfate, 0.16M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dehydrate pH 5.6
Resolution 1.50 Å R-free 0.211
6M3Q Crystal structure of AnkB/beta4-spectrin complex Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 951–1458（508 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；25% w/v pentaerythritol propoxylate 629 (17/8 PO/OH), 50 mM magnesium chloride and 0.1 M HEPES, pH 7.5
Resolution 3.44 Å R-free 0.307
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1699–1710（12 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000
Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1699–1710（12 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000
Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1699–1710（12 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000
Resolution 2.07 Å R-free 0.226
8ZE8 Arf-GTPase activating protein Asap1 SH3 domain in complex with 440 Kd Ankyrin-B fragment Deposited 2024-05-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1699–1710（12 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M MES monohydrate, pH=6.0, 20 % w/v Polyethylene glycol 6,000
Resolution 2.07 Å R-free 0.226

10 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ANK2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 21–265； UniProt 966–1210 Author chain A； PDBConstruct 266–581； UniProt 1253–1568

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4d8o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4d8o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4d8o
Deposition date deposition_date2012-01-11
Structure title titleCrystal Structure of the ankyrin-B ZU5-ZU5-UPA-DD tandem
Keywords keywordsZU5, UPA, death domain, supramodule, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.11 Å
Radius of gyration Rg (electron density) rg_electron27.22 Å
Forward intensity I(0) i053119500.00
Molecular weight molecular_weight56746.0 kDa
Excluded volume excluded_volume71190 ų
Envelope volume envelope_volume90840 ų
Hydration-shell volume shell_volume28631 ų
Envelope diameter envelope_diameter91.3 Å
Shell Rg shell_rg33.76 Å
Envelope Rg envelope_rg27.07 Å
Shape Rg shape_rg27.23 Å
Total Rg total_rg27.92 Å
Total atoms total_atoms3989
Residues n_residues509
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax88.5 Å
Rg (real space) rg_real28.05 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real5.3120e+07
I(0) uncertainty (real space) i0_real_error7.5420e+05
Rg (reciprocal space) rg_reciprocal28.07 Å
I(0) (reciprocal space) i0_reciprocal53120000.0000
Solution quality estimate total_estimate0.9072
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0 Å
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.636
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15090000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.942
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4d8oA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id4d8oA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology220 — Chondroitinase Ac; Chain A, domain 3
Homologous superfamily homologous superfamily30 —
Domain ID domain_id4d8oA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2660 —
Domain ID domain_id4d8oA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology533 — Death Domain, Fas
Homologous superfamily homologous superfamily10 — Death Domain, Fas
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8. Citations (1)

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9. Files and Curves (10)